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- PDB-2n21: Solution structure of complex between DNA G-quadruplex and G-quad... -

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Basic information

Entry
Database: PDB / ID: 2n21
TitleSolution structure of complex between DNA G-quadruplex and G-quadruplex recognition domain of RHAU
Components
  • ATP-dependent RNA helicase DHX36
  • DNA (5'-D(*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
KeywordsHYDROLASE/DNA / HYDROLASE-DNA complex
Function / homology
Function and homology information


positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / positive regulation of mRNA 3'-end processing / telomerase RNA stabilization / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / positive regulation of myeloid dendritic cell cytokine production / DEx/H-box helicases activate type I IFN and inflammatory cytokines production ...positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of cardioblast differentiation / positive regulation of mRNA 3'-end processing / telomerase RNA stabilization / positive regulation of telomere maintenance via telomere lengthening / pre-miRNA binding / G-quadruplex DNA unwinding / positive regulation of myeloid dendritic cell cytokine production / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RNA secondary structure unwinding / G-quadruplex DNA binding / positive regulation of dendritic spine morphogenesis / regulation of transcription by RNA polymerase III / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / positive regulation of telomere maintenance / positive regulation of cytoplasmic translation / cellular response to arsenite ion / telomerase RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / response to exogenous dsRNA / positive regulation of interferon-alpha production / regulation of embryonic development / positive regulation of transcription initiation by RNA polymerase II / ATP-dependent activity, acting on DNA / regulation of mRNA stability / DNA helicase activity / ossification / mRNA 3'-UTR binding / mRNA 5'-UTR binding / cytoplasmic stress granule / histone deacetylase binding / cellular response to UV / single-stranded DNA binding / double-stranded RNA binding / cellular response to heat / perikaryon / G-quadruplex RNA binding / spermatogenesis / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / DNA helicase / negative regulation of translation / RNA helicase activity / chromosome, telomeric region / cell differentiation / transcription cis-regulatory region binding / RNA helicase / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / innate immune response / dendrite / positive regulation of gene expression / magnesium ion binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, distance geometry, molecular dynamics
Model detailslowest energy, model1
AuthorsHeddi, B. / Cheong, V.V. / Martadinata, H. / Phan, A.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex.
Authors: Heddi, B. / Cheong, V.V. / Martadinata, H. / Phan, A.T.
History
DepositionApr 25, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references / Structure summary
Revision 1.2Feb 7, 2018Group: Experimental preparation / Category: pdbx_nmr_exptl_sample_conditions
Item: _pdbx_nmr_exptl_sample_conditions.pH / _pdbx_nmr_exptl_sample_conditions.temperature
Revision 1.3Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DHX36
B: DNA (5'-D(*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)8,0912
Polymers8,0912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ATP-dependent RNA helicase DHX36 / DEAH box protein 36 / G4-resolvase 1 / G4R1 / MLE-like protein 1 / RNA helicase associated with AU- ...DEAH box protein 36 / G4-resolvase 1 / G4R1 / MLE-like protein 1 / RNA helicase associated with AU-rich element ARE


Mass: 2360.802 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 53-70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX36, DDX36, KIAA1488, MLEL1, RHAU / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2U1, DNA helicase, RNA helicase
#2: DNA chain DNA (5'-D(*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')


Mass: 5730.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1512D 1H-1H NOESY
1613D HNCO
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D HNHA
11213D 1H-13C NOESY
11313D 1H-15N NOESY
11413D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.1-1 mM [U-100% 13C; U-100% 15N] entity_1-1, 0.1-1 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2, 10-70 mM potassium chloride-3, 10-20 mM potassium phosphate-4, ...Contents: 0.1-1 mM [U-100% 13C; U-100% 15N] entity_1-1, 0.1-1 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2, 10-70 mM potassium chloride-3, 10-20 mM potassium phosphate-4, 0.1-1 mM entity_1-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-100% 13C; U-100% 15N]0.1-11
mMDNA (5'-D(*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-20.1-11
mMpotassium chloride-310-701
mMpotassium phosphate-410-201
mMentity_1-50.1-11
Sample conditionsIonic strength: 0.9 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AMXBrukerAMX7002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorechemical shift assignment
X-PLOR NIHGoddardgeometry optimization
X-PLOR NIHGoddardrefinement
X-PLOR NIHGoddardchemical shift assignment
RefinementMethod: DGSA-distance geometry simulated annealing, distance geometry, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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